def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(
".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
flow = flowtk.Flow(workdir=options.workdir)
# Build work of GS task. Each gs_task uses different (ngkpt, tsmear) values
# and represent the starting point of the phonon works.
scf_work = flowtk.Work()
ngkpt_list = [[4, 4, 4], [8, 8, 8]] #, [12, 12, 12]]
tsmear_list = [0.01, 0.02] # , 0.04]
for ngkpt in ngkpt_list:
for tsmear in tsmear_list:
scf_input = make_scf_input(structure, ngkpt, tsmear, pseudos)
scf_work.register_scf_task(scf_input)
flow.register_work(scf_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [2, 2, 2] q-mesh.
# For each GS task, construct a phonon work that will inherit (ngkpt, tsmear) from scf_task.
for scf_task in scf_work:
ph_work = flowtk.PhononWork.from_scf_task(scf_task,
qpoints=[2, 2, 2],
is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
#pseudos = abidata.pseudos("12mg.pspnc", "5b.pspnc")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
#print(scf_input.pseudos)
return abilab.bandstructure_flow(workdir,
scf_input,
nscf_input,
dos_inputs=dos_inputs,
manager=options.manager)
def make_ecut_flow(structure_file=None, ecut_list = (10, 12, 14, 16, 18)):
"""
Build and return a `Flow` to perform a convergence study wrt to ecut.
Args:
structure_file: (optional) file containing the crystalline structure.
If None, crystalline silicon structure.
ecut_list: List of cutoff energies to be investigated.
"""
# Define the structure and add the necessary pseudos:
if structure_file is None:
multi = abilab.MultiDataset(structure=abidata.cif_file("si.cif"),
pseudos=abidata.pseudos("14si.pspnc"), ndtset=len(ecut_list))
workdir = "flow_Si_ecut_convergence"
else:
structure = abilab.Structure.from_file(structure_file)
pseudos = abilab.PseudoTable() ## todo fix this
multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=len(ecut_list))
workdir = "flow_" + structure.composition.reduced_formula + "_ecut_convergence"
# Add mnemonics to the input files.
multi.set_mnemonics(True)
# Global variables
multi.set_vars(tolvrs=1e-9)
multi.set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Here we set the value of ecut used by the i-th task.
for i, ecut in enumerate(ecut_list):
multi[i].set_vars(ecut=ecut)
return abilab.Flow.from_inputs(workdir=workdir, inputs=multi.split_datasets())
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(
".py", "").replace("run_", "flow_")
# Init structure from internal database.
structure = abidata.structure_from_ucell("MgB2")
# Our pseudopotentials.
pseudos = abilab.PseudoTable(["Mg-low.psp8", "B.psp8"])
flow = flowtk.Flow(workdir=options.workdir)
# Build work of GS task. Each gs_task uses different (ngkpt, tsmear) values
# and represent the starting point of the phonon works.
ngkpt = [12, 12, 12]
tsmear = 0.02
scf_input, nscf_input = make_scf_nscf_inputs(structure, ngkpt, tsmear,
pseudos)
gs_work = flowtk.Work()
scf_task = gs_work.register_scf_task(scf_input)
nscf_task = gs_work.register_nscf_task(nscf_input, deps={scf_task: "DEN"})
flow.register_work(gs_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [6, 6, 6] q-mesh.
ph_work = flowtk.PhononWork.from_scf_task(scf_task,
qpoints=[4, 4, 4],
is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
flow = flowtk.Flow(workdir=options.workdir)
scf_work = flowtk.Work()
ngkpt_list = [[4, 4, 4], [8, 8, 8], [12, 12, 12]]
tsmear_list = [0.01, 0.02, 0.04]
for ngkpt in ngkpt_list:
for tsmear in tsmear_list:
scf_input = make_scf_input(structure, ngkpt, tsmear, pseudos)
scf_work.register_scf_task(scf_input)
flow.register_work(scf_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [4, 4, 4] q-mesh.
for scf_task in scf_work:
ph_work = flowtk.PhononWork.from_scf_task(scf_task, qpoints=[4, 4, 4], is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
